1miv
Crystal structure of Bacillus stearothermophilus CCA-adding enzyme
SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
1. 结构基本信息 1. Structure Basics
| 条目编号 entry_id | 1miv |
| 沉积日期 deposition_date | 2002-08-23 |
| 结构标题 title | Crystal structure of Bacillus stearothermophilus CCA-adding enzyme |
| 关键词 keywords | CCA-adding enzyme, tRNA nucleotidyltransferase, TRANSLATION, TRANSFERASE; TRANSLATION, TRANSFERASE |
| 实验方法 method | X-RAY DIFFRACTION |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 35.75 Å |
| 回转半径 Rg (电子) rg_electron | 35.48 Å |
| 零角强度 I(0) i0 | 125590000.00 |
| 分子量 molecular_weight | 89303.0 kDa |
| 排除体积 excluded_volume | 111660 ų |
| 包络体积 envelope_volume | 160720 ų |
| 水化壳体积 shell_volume | 40180 ų |
| 包络直径 envelope_diameter | 144.4 Å |
| 壳层 Rg shell_rg | 39.18 Å |
| 包络 Rg envelope_rg | 35.44 Å |
| 形状 Rg shape_rg | 35.53 Å |
| 总 Rg total_rg | 35.59 Å |
| 总原子数 total_atoms | 6228 |
| 残基数 n_residues | 770 |
| 球谐函数阶数 n_harmonics | 20 |
| q 范围 q_range | — – 0.5000 Å−1 |
| 数据点数 n_points | 101 |
| 壳层类型 shell_type | directional |
| 溶剂电子密度 solvent_density | 0.3340 e/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| CRYSOL 版本 crysol_version | 4.1.3 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 136.0 Å |
| Rg (实空间) rg_real | 35.97 Å |
| Rg 误差 (实空间) rg_real_error | 1.55 Å |
| I(0) (实空间) i0_real | 1.2560e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.2470e+06 |
| Rg (倒空间) rg_reciprocal | 35.83 Å |
| I(0) (倒空间) i0_reciprocal | 125600000.0000 |
| 解质量估计 total_estimate | 0.5989 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 43.3 Å |
| 偏度 Skewness skewness | 0.543 |
| 峰度 Kurtosis kurtosis | 0.211 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 9103000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.648; Stabil: 1.000; Sysdev: 0.028; Positv: 1.000; Valcen: 0.790; Smooth: 0.966 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1miva1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.173 — Poly A polymerase C-terminal region-like |
| 超家族 Superfamily superfamily | a.173.1 — Poly A polymerase C-terminal region-like |
| 家族 Family family | a.173.1.1 — Poly A polymerase C-terminal region-like |
| 结构域编号 domain_id | d1miva2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.218 — Nucleotidyltransferase |
| 超家族 Superfamily superfamily | d.218.1 — Nucleotidyltransferase |
| 家族 Family family | d.218.1.4 — Poly A polymerase head domain-like |
| 结构域编号 domain_id | d1mivb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.173 — Poly A polymerase C-terminal region-like |
| 超家族 Superfamily superfamily | a.173.1 — Poly A polymerase C-terminal region-like |
| 家族 Family family | a.173.1.1 — Poly A polymerase C-terminal region-like |
| 结构域编号 domain_id | d1mivb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.218 — Nucleotidyltransferase |
| 超家族 Superfamily superfamily | d.218.1 — Nucleotidyltransferase |
| 家族 Family family | d.218.1.4 — Poly A polymerase head domain-like |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1mivA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 460 — Beta Polymerase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Beta Polymerase, domain 2 |
| 结构域编号 domain_id | 1mivA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 110 — Hydrophobic Seed Protein |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1mivA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 560 — |
| 结构域编号 domain_id | 1mivA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 246 — Serum Albumin; Chain A, Domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 80 — |
| 结构域编号 domain_id | 1mivB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 460 — Beta Polymerase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Beta Polymerase, domain 2 |
| 结构域编号 domain_id | 1mivB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 110 — Hydrophobic Seed Protein |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1mivB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 560 — |
| 结构域编号 domain_id | 1mivB04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 246 — Serum Albumin; Chain A, Domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 80 — |